Broken Base: Some fans complain that this game's action-RPG battle system is far inferior to those used in the previous two. It's a reasonable complaint, since it is less advanced than those of other games like Kingdom Hearts 2. The battle system is rather bare-bones as well, barring the reyvateil mechanic...really, there are a heck of a lot of ways they could've made the battle system better.
East or West, every Ar Tonelico 3 player's complaint for this game is likely to be "Why won't Akane join us?!" She's a gorgeous Lady of War,Finnel's best friend, and regularly travels with the group in Phase IV. The answer is likely the additional resources to make the FMV for her special attack, making the purged model, making additional party topics, and drawing up the artwork for new weapons and armors. The same applies for any other character that could have joined.
Then, of course, there's Cocona, who was guaranteed a role in this game due to her dark horse status in AT 2.
Inferred Holocaust: Ar Ciel dying one year later after the game unless the AAA Project is carried out successfully. This means that if the player ends the game with any ending but the True ones, the planet will break apart, and everything in it will die.Word of God even went on to write a complete description for this!
Informed Wrongness: Shurelia has done something that makes Tyria hates her, but they never shows it and Shurelia is just mentioned in 2 lines in this game, Sequel Hook perhaps? Answer in the manual (and the note) note It's because she envied the kind of father Shurelia had: Eleno (Shurelia's adoptive father) treated her with love and kindness, while Kurogane (Tyria's adoptive father and creator) treated her as a guinea pig and forced her to undergo cruel and horrible experiments to bring about her true potential.
Magnificent Bastard: Akane, she purposely let Archia hack Clustenia's database to lead them to the wrong place; later she takes this chance to catch our heroes and the said Archia's second in command, and proceeds to invade Archia while they're unaware. She's a great example of an intelligent antagonist; Ensemble Darkhorse indeed!
XaaaCi...or a Tear Jerker, if you read the last few lyric lines and what the song is supposed to represent: Gaia's Vengeance at its finest. Few things are so tear-inducing as getting told by the Planet itself how much damage you have done to it, and if you still remember the days in which she it gave you so much.
Sakia Lumei is the original personality of Saki's body. Instead of exploring her past, feelings about her only purpose to be a vessel, and possible conflict between her and Saki, the game never brings it up. Instead, Sakia becomes the designated big sister while the main conflict in Saki's Cosmosphere is her Refusal of the Call. However, in the second light novel it becomes apparent she never had any intention of regaining control of her body because she didn't want Saki, who had a much more fragile personality than herself, to go through the same experience of being forced to sleep indefinitely without anyone being aware of her existence.
Luphan/Ayatane is another wasted character. He's a descendant of the Teru Tribe who caused the Grathnode Inferia (AKA the reason the surface is destroyed). Rather than go into his background or have him join the party as the designated Teru with dual katanas, all he gets to do is become the first game's Ayatane pre-Heel–Face Turn and die praising Reyvateilia. Granted, there was no way they could have gotten him to join the party due the his burning hatred for the humans due to the fact his family and all the other Teru were massacred by Archia several decades prior to the start of the game, and that unlike the first game's Ayatane who was only following Mir's orders, this Ayatane actually wanted them dead out of his own will.
Aoto, at least in Tyria's True ending. The girl that he loves is going to die within a year and there is nothing that he can do about it just so the world will be safe. note At least until the light novels and her Drama CD came around, which shows that Tyria was indeed saved, although that cost the very existence of the Third Tower and almost all of the Second Tower's Rim.
Finnel, who is put through a ton of suffering from birth to near the end of the game.
Tyria herself also counts as while she didn't think anything of it, Shurelia considered her upbringing the very definition of hell. Also, in the novels she suffered a lot due to the life extension treatment she was forced to undergo, and finally her life ended right when Sasha was completing the song that would have allowed to undo her Tower transformation and continue living without suffering. Luckily she got better, but before that point, it was an endless series of painful events one after other.